Fluorescence lifetime is an important characteristic parameter of quantum dot, which plays an important role in studying the optical properties of quantum dot. As a common method to obtain fluorescence lifetime, fluorescence decay curve fitting has been broadly accepted. The least squares fitting to the fluorescence decay curve is performed by using the exponential decay function to obtain fluorescence lifetime with taking the instrument response function into account. However, since the fluorescence decay curve inevitably involves noise photons such as dark counts and stray photons, there is a certain error in the fluorescence lifetime obtained by the method. In order to reduce the error and improve the accuracy of the results, enough photons are required. Nevertheless, too many photons will result in low efficiency of lifetime analysis and temporal resolution, and therefore this method can hardly extract dynamic information on a smaller temporal scale. In this paper, we propose a new method of obtaining the fluorescence lifetime of quantum dot, namely the single photons modulation spectrum. The basic idea is based on the relationship between the fluorescence lifetime and the signal amplitude of pulse repetition frequency in a single dynamic process. The experimental results show that the fluctuation errors and deviation errors of lifetime obtained by our method are significantly lower than those of the previous method when the same number of photons is used. Therefore, high-accuracy fluorescence lifetime can be obtained. When the fluctuation error is 5%, the accuracy is increased by more than one order of magnitude. And to obtain the fluorescence lifetime of the same error level, the number of photons required for our method is much smaller than that of the previous one, which indicates that our method can effectively suppress the disturbance of noise photons and enables the lifetime measurement with high efficiency and temporal resolution. When the fluctuation error and deviation error are both 5%, the efficiency and temporal resolution are increased by more than four times. Finally, real-time lifetime trajectory corresponding to the photoluminescence intensity time trajectory is obtained by our method, where rich dynamic information can be obtained on a sub-second temporal scale. The method of obtaining fluorescence lifetime with powerful anti-noise capability, high efficiency and temporal resolution proposed in this paper can play an important role in studying the fluorescence dynamics of single quantum systems.